Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010244.1 Corchorus olitorius cultivar O-4 contig10276, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 3209
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29


Found at i:1038 original size:16 final size:15

Alignment explanation


    Indices: 999--1040  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        989 ACAGAGATTG

                   *       
        999 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

              *            
       1014 ACGGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1029 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1041 AGCAAAGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.62, C:0.14, G:0.12, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:2939 original size:22 final size:22

Alignment explanation


    Indices: 2908--2951  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2898 TTCTTTCCGC

                       *          
       2908 AACAACTTCTGTCCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

                 *      *         
       2930 AACAAGTTCTGGGCCGAAGTTG
          1 AACAACTTCTGGCCCGAAGTTG

       2952 TCCTGCGCAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25


Consensus pattern (22 bp):   
AACAACTTCTGGCCCGAAGTTG

Found at i:2962 original size:52 final size:52

Alignment explanation


    Indices: 2905--3005  Score: 177
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       2895 TTTTTCTTTC

                           *                                     
       2905 CGCAACAA-CTTCTGTCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG
          1 CGCAACAACCTT-TGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG

                                                             
       2957 CGCAACAACCTTTGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTC
          1 CGCAACAACCTTTGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTC

       3006 TTGCAAATCT


Statistics
Matches: 47,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  52   44  0.94
  53    3  0.06

ACGTcount: A:0.24, C:0.28, G:0.25, T:0.24


Consensus pattern (52 bp):   
CGCAACAACCTTTGCCCCGAAGTTGAACAAGTTCTGGGCCGAAGTTGTCCTG

Found at i:3059 original size:21 final size:21

Alignment explanation


    Indices: 3035--3075  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3025 TTCGACAGGC

                *                
       3035 CAACTTCTGGGCAGAAGTTGA
          1 CAACATCTGGGCAGAAGTTGA

                        *       
       3056 CAACATCTGGGCTGAAGTTG
          1 CAACATCTGGGCAGAAGTTG

       3076 TCTTGTATTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24


Consensus pattern (21 bp):   
CAACATCTGGGCAGAAGTTGA
Done.